Polymorphism of Human Papillomavirus Type 31 Isolates Infecting the Genital Tract of HIV-Seropositive and HIV-Seronegative Women at Risk for HIV Infection

The genomic polymorphism of high-risk human papillomavirus (HPV) for types other than 16 has not been extensively described. We describe here the genomic polymorphism of high-risk HPV type 31 in 79 women (62 HIV-seropositive, 17 HIV-seronegative) by PCR-sequencing of the long control region (LCR), E6 and E7. LCR polymorphism was generated by 25 (6.4%) single-nucleotide variations over 391 bases. Each variant compared to the prototype contained from 2 to 13 variations (mean of 9.4 3.3, median of 10). Considering the number of variation sites in each region of the HPV genome, the LCR was more variable than E6 (13 over 496 nucleotide (nt), P¼ 0.03) and E7 (9 over 296 nt, P¼ 0.03). Non-synonymous nucleotide variations were found in 31 (75.6%) of 41 isolates and were observed at six positions in E6. Each of the 8 HPV-31 E7 variants contained from 2 to 5 mutations (mean of 4.29 1.11, median of 5) compared to the prototype. Three non-synonymous E6 and E7 variations were within cysteine arrays. The LCR prototype was significantly overrepresented in Caucasian women (14 (25%) of 56) compared to women of African descent (0 (0%) of 15 women, P¼ 0.03). Four (23.5%) of 17 women with persistent versus 6 (25.0%) of 24 women with transient infections were infected by the prototype (P¼ 1.00). HPV-31 LCR was more polymorphic than oncogenes and was associated with ethnicity.